Research workbench
Crystal structure of a probable oxidoreductase yhhx in triclinic form. northeast structural genomics target ER647
Analyse Crystal structure of a probable oxidoreductase yhhx in triclinic form.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F4L
- Type
- protein
- Length
- 2,064 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase yhhx
- EC
- 1.-.-.-
- UniProt
- P46853
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Putative oxidoreductase yhhx (EC 1.-.-.-) | protein | 344 | 34% helix, 25% strand | P46853 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.62 | 0.77 | 54 | empty |
| 2 | 390 | 0.62 | 0.77 | 57 | empty |
| 3 | 389 | 0.60 | 0.76 | 56 | empty |
| 4 | 353 | 0.59 | 0.76 | 55 | empty |
| 5 | 325 | 0.58 | 0.76 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–F · 1769 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1750 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1739 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3F4L · Crystal structure of a probable oxidoreductase yhhX in Triclinic form. Northeast… · the same entry in another collection · chain C against C, TM-score 1.00
- P46853 · AlphaFold monomer V2.0 prediction for uncharacterized oxidoreductase yhhx (P46853) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P46853
- Elsewhere: RCSB PDB 3F4L · PDBe 3F4L · UniProt P46853
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